Whole-genome analysis of vancomycin-resistant Enterococcus faecium causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavaria, Germany.

OBJECTIVES: Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) represent a major public health concern due to limited treatment options. Among invasive isolates of VREfm, ST117, ST80 and ST78 represent the most frequently detected STs by MLST in Germany. In this study, we investigated the genetic diversity of isolates of VREfm recovered from different nosocomial outbreaks in Bavaria, Germany, by WGS. METHODS: Between January 2018 and April 2019, 99 non-replicate isolates of VREfm originating from nosocomial outbreaks at eight different hospitals in Bavaria were investigated for genetic diversity by WGS. In detail, complex types (CTs) were identified by core-genome MLST. Furthermore, an SNP analysis was performed for all VREfm strains. RESULTS: Most of the isolates of this study (76%) belonged to three major clonal groups, which occurred in at least three hospitals: ST80/CT1065 vanB (n = 45; six hospitals), ST117/CT71 vanB (n = 11; four hospitals) and ST78/CT894like vanA (n = 19; three hospitals). Moreover, isolates of the predominant lineage ST80/CT1065 vanB showed a maximum difference of 36 SNPs as revealed by SNP analysis. CONCLUSIONS: Whole-genome analysis of VREfm causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavarian hospital settings, namely ST80/CT1065 vanB, ST117/CT71 vanB and ST78/CT894like vanA. Further studies are needed for a better understanding of the factors affecting the successful spread of the above-mentioned lineages.

Extended-spectrum-ß-lactamase-producing Escherichia coli as intestinal colonizers in the German community.

We determined the presence of extended-spectrum-ß-lactamase (ESBL)-producing Escherichia coli among 3,344 study participants from the German community. Intestinal colonization was detected in 211 persons (6.3%), without significant differences among the different age groups. The majority (95.2%) of isolates harbored CTX-M-type ESBL, with CTX-M-15 (46%) and CTX-M-1 (24.2%) as the most common types. The finding of ESBL producers and one isolate additionally producing carbapenemase OXA-244 indicates a risk of dissemination of resistant bacteria outside the hospitals.

High prevalence of the recently identified clonal lineage ST1299/CT3109 vanA among vancomycin-resistant Enterococcus faecium strains isolated from municipal wastewater.

Previously, we demonstrated that the majority of vancomycin-resistant Enterococcus faecium (VREfm) strains from in-patients of the University Hospital Erlangen, Germany, belonged to only three clonal lineages, namely ST117/CT71 vanB and two novel ST1299 vanA lineages classified as CT3109 and CT1903. The goal of the current study was (i) to investigate whether VREfm is also detectable in wastewater of the city of Erlangen, (ii) to identify their molecular features, and (iii) to clarify whether VREfm could arise from the community of the city of Erlangen or can be (directly) connected to nosocomial infections in the hospital setting. From April to May 2023, a total of 244 VREfm strains from raw wastewater of the city of Erlangen were analyzed by core genome multilocus sequence typing (cgMLST). Moreover, 20 of them were further investigated for single nucleotide polymorphisms (SNPs). The molecular characterization of the wastewater VREfm strains revealed a high prevalence (27.9%) of the recently identified clonal lineage ST1299/CT3109 vanA, which is mainly characterized by the presence of the tetracycline-resistance determinant tet(M) and the virulence genes pilA and prpA. The SNPs analysis revealed the presence of two major clusters, namely cluster I (≤65 SNPs), which included well-known hospital-adapted vanB clonal lineages such as ST117/CT71 and ST80/CT1065 and cluster II (≤70 SNPs), which were mainly characterized by the lineage ST1299/CT3109 vanA. Based on the concomitant resistance to vancomycin and tetracycline, we propose that ST1299/CT3109 vanA primarily originated and spread outside of hospital settings.IMPORTANCEThis study provides a detailed genomic analysis of vancomycin-resistant Enterococcus faecium (VREfm) strains isolated from municipal wastewater with a particular focus on clonal lineages, antimicrobial resistance, and the presence of virulence genes. The high wastewater prevalence of the recently identified clonal lineage ST1299/CT3109 vanA, which has been previously detected in hospitals, suggests an enormous potential for future spread in Germany.

First report of the new emerging global clone ST1193 among clinical isolates of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli from Germany.

OBJECTIVES: Sequence type 1193 (ST1193) is a new emerging global clone of Escherichia coli. The main goal of this study was to determine the prevalence and molecular characteristics of ST1193 among clinical isolates of extended-spectrum ß-lactamase (ESBL)-producing E. coli from University Hospital of Erlangen, Germany. METHODS: Between November 2015 and February 2016, all consecutive non-duplicate clinical E. coli isolates showing resistance to cefotaxime or ceftazidime were further analysed for ESBL production by the combined disk method. ESBL genes were identified by PCR and sequencing. Bacterial strain typing was performed by PCR-based phylogrouping, MLST and whole-genome sequencing. RESULTS: ESBL production was confirmed in 51 isolates. The globally dominant ST131 occurred at a frequency of 37.3% (n=19). Major non-ST131 sequence types were ST38 (n=4; 7.8%), ST10 (n=3; 5.9%) and ST1193 (n=3; 5.9%). Among the ESBL-producing E. coli ST1193, two expressed CTX-M-14 and one expressed CTX-M-15 ESBL type. All three ST1193 isolates belonged to serogroup O75:H5, phylogroup B2, and harboured IncFIA and IncFIB plasmids and the virulence factors genes iha, sat, gad, vat and senB. Moreover, they showed ciprofloxacin resistance and exhibited a set of four conserved mutations defining quinolone resistance (gyrA S83L, gyrA D87N, parC S80I and parC L416F). CONCLUSIONS: This study revealed for the first time in Germany the occurrence of ST1193 among clinical isolates of ESBL-producing E. coli. Further national or regional multicentre studies are needed to assess the effective relevance of ESBL-producing E. coli ST1193 as a nosocomial pathogen in Germany.

Prevalence and genetic diversity of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli in nursing homes in Bavaria, Germany.

Main goal of this study was to determine the prevalence and molecular epidemiology of extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae among 156 nursing home residents in Bavaria and to compare the results with healthy individuals from the Bavarian community. Intestinal colonisation by ESBL-producing Escherichia coli was detected in 23 nursing home residents (14.7%) using MacConkey agar supplemented with cefotaxime (1mg/L) for screening and the combined disc method for ESBL confirmation. Antimicrobial susceptibility testing revealed co-resistance to ciprofloxacin in 86.9% of the ESBL-producers. All isolates harboured CTX-M-ESBL with CTX-M-15 (65.2%) and CTX-M-27 (21.7%) as the most common types. Moreover, 16 isolates (69.6%) could be assigned by PCR-typing to the epidemic clonal lineage E. coli O25b-ST131. Further typing by rep-PCR and XbaI-macrorestriction with subsequent pulsed-field gel electrophoresis, respectively, revealed that two or more residents shared the same ESBL-producing E. coli clone in four nursing homes. In conclusion, we could show a high prevalence of ESBL-producing E. coli in Bavarian nursing homes (14.7%) compared to the healthy population (6.3%). Although the prevalence of ESBL-type CTX-M-15 in E. coli was similar in nursing home residents (65.2%) and healthy individuals (46%) the presence of E. coli O25b-ST131 clones differed substantially (69.6% and 14.2%, respectively). Furthermore, this study demonstrates that a person-to-person transmission or a common source of infection for ESBL-producing microorganisms may occur in these facilities. Therefore, basic hygiene measures should be assiduously implemented to prevent the further spread of these multidrug-resistant bacteria.

Screening of ESBL-producing Enterobacteriacae concomitant with low degree of transmission in intensive care and bone marrow transplant units.

BACKGROUND: Extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-E) are spreading worldwide in both hospital and community settings. In this study, the molecular epidemiology and the transmission modalities of ESBL-E in intensive care- and bone marrow transplant were investigated. METHODS: All patients included in this study were screened for presence of ESBL-E on admission and weekly. Relevant ß-lactamase genes were identified by PCR and sequencing. RESULTS: A total of 669 patients were included in this study. On admission, ESBL-producing Escherichia coli were detected in 49 (7.3%) patients and ESBL-producing Klebsiella pneumoniae in one patient. The most common ESBL types among E. coli isolates were CTX-M-15 (38.8%) and CTX-M-1 (38.8%). Furthermore, 12 of 49 (24.5%) ESBL-producing E. coli could be assigned to the epidemic clone ST131. A single patient acquired ESBL-producing E. coli during the hospital stay but cross-transmission could not be demonstrated. Among 1095 environmental samples none revealed ESBL. CONCLUSIONS: Our results suggest that early detection of ESBL-producing Enterobacteriaceae and consequent implementation of basic hygiene measures and contact isolation may reduce the transmission rate during the hospital stay.

Prevalence, antimicrobial susceptibility, and genetic diversity of Pseudomonas aeruginosa as intestinal colonizer in the community.

In this study we determined the prevalence of intestinal carriage, the antimicrobial susceptibility rates, and the genetic diversity of Pseudomonas aeruginosa in the community. From July 2010 to December 2011, a total of 2110 nonreplicate fecal samples from individuals living in Bavaria were collected. Samples were screened for P. aeruginosa by a selective medium and antimicrobial susceptibility was determined by disc diffusion technique. Genetic diversity was assessed by multilocus sequence typing (MLST). Intestinal colonization was detected in 31 of 2110 (1.47%) individuals. None of the isolates showed resistance to aztreonam, imipenem, meropenem, ciprofloxacin, amikacin or colistin. Twenty-five isolates could be assigned to 20 different sequence types (STs), whereas the remaining 6 could not be assigned. Interestingly, four isolates belonged to ST253. These data show that intestinal colonization by P. aeruginosa occurs in the community with high genetic diversity and low rates of antimicrobial resistance.